AutoCloner

Multiple sequence alignment - TraesCS3D01G361600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS3D01G361600	chr3D	100.000	4339	0	0	1	4339	475441505	475445843	0.000000e+00	8013.0
1	TraesCS3D01G361600	chr3D	88.332	1457	122	28	627	2056	475587580	475589015	0.000000e+00	1705.0
2	TraesCS3D01G361600	chr3D	85.094	1543	138	51	2117	3600	475589601	475591110	0.000000e+00	1491.0
3	TraesCS3D01G361600	chr3D	83.563	1235	121	39	777	1959	475550161	475551365	0.000000e+00	1081.0
4	TraesCS3D01G361600	chr3D	96.629	445	12	1	2485	2929	475551703	475552144	0.000000e+00	736.0
5	TraesCS3D01G361600	chr3D	87.175	616	61	10	2987	3590	475552139	475552748	0.000000e+00	684.0
6	TraesCS3D01G361600	chr3D	88.272	162	15	3	606	763	475549956	475550117	1.590000e-44	191.0
7	TraesCS3D01G361600	chr3D	94.203	69	4	0	3472	3540	475552759	475552827	5.930000e-19	106.0
8	TraesCS3D01G361600	chr3D	93.333	60	4	0	517	576	475549569	475549628	5.980000e-14	89.8
9	TraesCS3D01G361600	chr3D	100.000	30	0	0	2061	2090	475589041	475589070	6.060000e-04	56.5
10	TraesCS3D01G361600	chr3B	97.097	3204	86	5	1	3200	632118565	632121765	0.000000e+00	5395.0
11	TraesCS3D01G361600	chr3B	88.480	1493	125	28	627	2090	632547287	632548761	0.000000e+00	1760.0
12	TraesCS3D01G361600	chr3B	85.549	1557	142	44	2107	3599	632549321	632550858	0.000000e+00	1552.0
13	TraesCS3D01G361600	chr3B	85.422	1221	112	37	777	1960	632202895	632204086	0.000000e+00	1208.0
14	TraesCS3D01G361600	chr3B	89.474	684	60	7	2451	3124	632204416	632205097	0.000000e+00	854.0
15	TraesCS3D01G361600	chr3B	95.643	482	13	4	3151	3631	632121758	632122232	0.000000e+00	767.0
16	TraesCS3D01G361600	chr3B	92.691	301	17	1	3810	4105	632138768	632139068	3.100000e-116	429.0
17	TraesCS3D01G361600	chr3B	96.196	184	7	0	3630	3813	632122270	632122453	7.050000e-78	302.0
18	TraesCS3D01G361600	chr3B	83.451	284	33	10	484	763	632202577	632202850	7.200000e-63	252.0
19	TraesCS3D01G361600	chr3B	87.293	181	17	4	3419	3593	632205798	632205978	7.360000e-48	202.0
20	TraesCS3D01G361600	chr3B	88.095	126	9	4	3472	3591	632205986	632206111	1.260000e-30	145.0
21	TraesCS3D01G361600	chr3B	85.859	99	7	6	396	490	78752384	78752479	9.930000e-17	99.0
22	TraesCS3D01G361600	chr3A	95.484	3078	90	15	562	3631	618163932	618166968	0.000000e+00	4868.0
23	TraesCS3D01G361600	chr3A	95.397	717	23	3	3630	4339	618167004	618167717	0.000000e+00	1133.0
24	TraesCS3D01G361600	chr3A	90.504	337	15	9	1	330	618163602	618163928	3.100000e-116	429.0
25	TraesCS3D01G361600	chr5D	93.750	64	3	1	429	492	451882166	451882104	1.280000e-15	95.3
26	TraesCS3D01G361600	chr4D	95.000	60	2	1	431	490	120832617	120832559	4.620000e-15	93.5
27	TraesCS3D01G361600	chr7D	94.737	57	1	1	431	485	13311063	13311007	2.150000e-13	87.9
28	TraesCS3D01G361600	chr7D	92.063	63	2	3	429	490	518794466	518794526	7.730000e-13	86.1
29	TraesCS3D01G361600	chr5B	92.063	63	2	3	426	485	712433552	712433490	7.730000e-13	86.1
30	TraesCS3D01G361600	chr7B	91.667	60	5	0	430	489	538386701	538386642	2.780000e-12	84.2
31	TraesCS3D01G361600	chr4A	86.585	82	4	4	426	500	741472618	741472537	2.780000e-12	84.2

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS3D01G361600	chr3D	475441505	475445843	4338	False	8013.000000	8013	100.000000	1	4339	1	chr3D.!!$F1	4338
1	TraesCS3D01G361600	chr3D	475587580	475591110	3530	False	1084.166667	1705	91.142000	627	3600	3	chr3D.!!$F3	2973
2	TraesCS3D01G361600	chr3D	475549569	475552827	3258	False	481.300000	1081	90.529167	517	3590	6	chr3D.!!$F2	3073
3	TraesCS3D01G361600	chr3B	632118565	632122453	3888	False	2154.666667	5395	96.312000	1	3813	3	chr3B.!!$F3	3812
4	TraesCS3D01G361600	chr3B	632547287	632550858	3571	False	1656.000000	1760	87.014500	627	3599	2	chr3B.!!$F5	2972
5	TraesCS3D01G361600	chr3B	632202577	632206111	3534	False	532.200000	1208	86.747000	484	3593	5	chr3B.!!$F4	3109
6	TraesCS3D01G361600	chr3A	618163602	618167717	4115	False	2143.333333	4868	93.795000	1	4339	3	chr3A.!!$F1	4338

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
821	1171	2.666190	GCGCAACAGCTGACCTCA	60.666	61.111	23.35	0.00	0.0	3.86	F
1717	2110	0.796312	GATGGACAAATCACGTGCGT	59.204	50.000	11.67	5.02	0.0	5.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2299	3343	0.962356	AATGGCCTGGCTGAAACTCG	60.962	55.0	19.68	0.0	0.0	4.18	R
3606	5243	2.545526	CCTAGCTCAACACACAACACAG	59.454	50.0	0.00	0.0	0.0	3.66	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	6.088085	CACGAAAAGAACAAGTTGCATATTCC	59.912	38.462	1.81	0.00	0.00	3.01
52	53	5.730550	AGAACAAGTTGCATATTCCGACTA	58.269	37.500	1.81	0.00	0.00	2.59
170	171	8.157476	ACCACTTTTCACATGACTCTTTAGTAT	58.843	33.333	0.00	0.00	35.56	2.12
340	350	5.850557	TGTGTGGAATGTTCATGAAGTTT	57.149	34.783	8.80	5.44	0.00	2.66
353	363	7.451255	TGTTCATGAAGTTTATTGGAACTGGAT	59.549	33.333	8.80	0.00	39.68	3.41
354	364	7.630242	TCATGAAGTTTATTGGAACTGGATC	57.370	36.000	0.00	0.00	39.68	3.36
393	403	8.926715	ATTGTTTTACTTGAAGACCAAAGAAC	57.073	30.769	0.00	0.00	33.76	3.01
394	404	7.455641	TGTTTTACTTGAAGACCAAAGAACA	57.544	32.000	0.00	0.00	33.76	3.18
447	457	5.954150	ACATAAGTACTCCCTCCGTAAAGAA	59.046	40.000	0.00	0.00	0.00	2.52
457	467	4.093850	CCCTCCGTAAAGAAATACCAAACG	59.906	45.833	0.00	0.00	0.00	3.60
821	1171	2.666190	GCGCAACAGCTGACCTCA	60.666	61.111	23.35	0.00	0.00	3.86
1060	1420	2.361737	GCCTTCTTCCCTGTGCCC	60.362	66.667	0.00	0.00	0.00	5.36
1512	1901	3.444388	AGGAAGAGGATGAGTACGTGAAC	59.556	47.826	0.00	0.00	0.00	3.18
1523	1912	2.000447	GTACGTGAACCAGCTGAATCC	59.000	52.381	17.39	6.26	0.00	3.01
1604	1997	5.521010	TCAATTTGCTTTCTTGTTTGCAGAG	59.479	36.000	0.00	0.00	36.75	3.35
1717	2110	0.796312	GATGGACAAATCACGTGCGT	59.204	50.000	11.67	5.02	0.00	5.24
2294	3338	9.968743	CAATTTCTAACGACTATTTGTTACTCC	57.031	33.333	0.00	0.00	31.28	3.85
2297	3341	8.752766	TTCTAACGACTATTTGTTACTCCTTG	57.247	34.615	0.00	0.00	31.28	3.61
2299	3343	4.251268	ACGACTATTTGTTACTCCTTGCC	58.749	43.478	0.00	0.00	0.00	4.52
2398	3468	5.065988	AGCGACGCAATTTATTTCTACCAAT	59.934	36.000	23.70	0.00	0.00	3.16
2515	3585	2.203470	TGCTTGTGCCAATCATCTGA	57.797	45.000	0.00	0.00	38.71	3.27
3371	4875	4.799419	TTGTCGTTTTTACCTTTCCGAG	57.201	40.909	0.00	0.00	0.00	4.63
3383	4887	7.982761	TTACCTTTCCGAGCATTTTACTTTA	57.017	32.000	0.00	0.00	0.00	1.85
3403	4913	2.363306	TGGTTGGTTCAATCTGCTGT	57.637	45.000	0.00	0.00	0.00	4.40
3422	5048	3.150767	TGTTGTTGTATACTGTTGCCCC	58.849	45.455	4.17	0.00	0.00	5.80
3580	5217	5.237344	CGATTCACCCTATGGATTTCTGTTC	59.763	44.000	0.00	0.00	34.81	3.18
3594	5231	6.202954	GGATTTCTGTTCCCGACATTATACTG	59.797	42.308	0.00	0.00	37.69	2.74
3667	5345	0.467804	GGAGCAGGGACTTCATCTCC	59.532	60.000	0.00	0.00	34.60	3.71
3727	5405	2.485814	GTCTTTGATCTTGCTCACCACC	59.514	50.000	0.00	0.00	0.00	4.61
3739	5417	0.526211	TCACCACCGACTGAGAATCG	59.474	55.000	0.00	0.00	38.61	3.34
3819	5497	3.712907	GGGCCAGTAGTTCCGCCA	61.713	66.667	4.39	0.00	43.50	5.69
3820	5498	2.590092	GGCCAGTAGTTCCGCCAT	59.410	61.111	0.00	0.00	41.25	4.40
3821	5499	1.523938	GGCCAGTAGTTCCGCCATC	60.524	63.158	0.00	0.00	41.25	3.51
3847	5525	1.059098	TCAGCAGCAGAGGGAAAGAA	58.941	50.000	0.00	0.00	0.00	2.52
3912	5590	2.756283	CTCCCCGCTCCGAAGTCT	60.756	66.667	0.00	0.00	0.00	3.24
3919	5597	1.139947	GCTCCGAAGTCTAGCGCTT	59.860	57.895	18.68	0.00	0.00	4.68
3961	5639	1.606601	GCCTTCACCCAAACCCTCC	60.607	63.158	0.00	0.00	0.00	4.30
3968	5646	1.265454	ACCCAAACCCTCCTCTAGCG	61.265	60.000	0.00	0.00	0.00	4.26
3988	5666	1.302832	GCACCACTTCTCCACCAGG	60.303	63.158	0.00	0.00	0.00	4.45
4059	5737	1.262417	TTCAGTCGGAGCACCATGTA	58.738	50.000	0.00	0.00	35.59	2.29
4097	5775	2.045047	TCTTCCATCTTCTGGTCCTCCT	59.955	50.000	0.00	0.00	46.08	3.69
4124	5802	4.561606	CACAATTCCTAGAACGTAGAACCG	59.438	45.833	0.00	0.00	0.00	4.44
4160	5839	2.143925	GTGTAGCACCACAACCTTCTC	58.856	52.381	1.31	0.00	35.38	2.87
4209	5888	1.327764	GCATCCAGCTGCGTAACTTAC	59.672	52.381	8.66	0.00	41.15	2.34
4255	5934	5.789643	AACTCAAAACATGGTGTAGCAAT	57.210	34.783	0.00	0.00	0.00	3.56
4282	5961	1.202510	GCTCAGCTCCATCCAGTACAG	60.203	57.143	0.00	0.00	0.00	2.74
4305	5990	1.756375	CGAGCAGGTGCATAAGCGAC	61.756	60.000	4.48	0.00	46.23	5.19
4333	6018	3.367646	AGTCTCCTCTCGACCATACAA	57.632	47.619	0.00	0.00	31.83	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
52	53	3.068307	CCTCGGGATCTATGAAAACGACT	59.932	47.826	0.00	0.00	0.00	4.18
457	467	8.425703	ACTCCCTCTGTAAAGAAATATAAGAGC	58.574	37.037	0.00	0.00	0.00	4.09
492	502	3.815401	CCATAGAAAAGCCCATTCCGTAG	59.185	47.826	0.00	0.00	0.00	3.51
621	929	5.551233	ACTCTTTTCAGTGGAATTCGATCA	58.449	37.500	0.00	0.00	31.93	2.92
821	1171	3.054802	CCAGGAGTAGCCAGTTTTCTCAT	60.055	47.826	0.00	0.00	40.02	2.90
969	1329	1.303309	CCGCCTCAGCCTTTAATCTG	58.697	55.000	0.00	0.00	34.57	2.90
1060	1420	2.242196	AGAGAGAGAGGGGAAGAGTCTG	59.758	54.545	0.00	0.00	0.00	3.51
1512	1901	0.108615	AACGACTCGGATTCAGCTGG	60.109	55.000	15.13	0.00	0.00	4.85
1604	1997	3.131223	TCATCGACCAATCTCCTGAGAAC	59.869	47.826	0.20	0.00	41.36	3.01
1717	2110	1.224315	CATCACCTTGATGCCGGGA	59.776	57.895	2.18	0.00	46.37	5.14
2262	3306	9.010029	ACAAATAGTCGTTAGAAATTGAATGGT	57.990	29.630	0.00	0.00	0.00	3.55
2278	3322	3.306166	CGGCAAGGAGTAACAAATAGTCG	59.694	47.826	0.00	0.00	35.17	4.18
2281	3325	4.504858	ACTCGGCAAGGAGTAACAAATAG	58.495	43.478	2.85	0.00	45.14	1.73
2299	3343	0.962356	AATGGCCTGGCTGAAACTCG	60.962	55.000	19.68	0.00	0.00	4.18
2398	3468	8.238631	GTGGTAGTTTTTCAAATTCGCCTTATA	58.761	33.333	0.00	0.00	0.00	0.98
3371	4875	7.954788	TTGAACCAACCATAAAGTAAAATGC	57.045	32.000	0.00	0.00	0.00	3.56
3383	4887	2.880443	ACAGCAGATTGAACCAACCAT	58.120	42.857	0.00	0.00	0.00	3.55
3403	4913	3.510531	TGGGGCAACAGTATACAACAA	57.489	42.857	5.50	0.00	39.74	2.83
3580	5217	3.026630	ACGATGCAGTATAATGTCGGG	57.973	47.619	14.90	1.51	33.75	5.14
3606	5243	2.545526	CCTAGCTCAACACACAACACAG	59.454	50.000	0.00	0.00	0.00	3.66
3739	5417	3.427309	GAAGCTCTTCCACGAGACC	57.573	57.895	0.00	0.00	33.64	3.85
3912	5590	0.442310	GTGCAATGTCGAAAGCGCTA	59.558	50.000	12.05	0.00	37.46	4.26
3919	5597	1.643868	GGCGATGGTGCAATGTCGAA	61.644	55.000	16.91	0.00	36.25	3.71
3961	5639	1.153549	GAAGTGGTGCCCGCTAGAG	60.154	63.158	7.60	0.00	44.35	2.43
3968	5646	2.034221	GGTGGAGAAGTGGTGCCC	59.966	66.667	0.00	0.00	0.00	5.36
4059	5737	3.341823	GAAGATCCAGTGCAAGTCATGT	58.658	45.455	0.00	0.00	0.00	3.21
4097	5775	6.519679	TCTACGTTCTAGGAATTGTGCTAA	57.480	37.500	0.00	0.00	0.00	3.09
4124	5802	1.884235	ACACAGCTTGTAGGAGTTGC	58.116	50.000	0.44	0.00	36.32	4.17
4209	5888	1.947678	GCCAGATGTTGACTCCCACTG	60.948	57.143	0.00	0.00	0.00	3.66
4255	5934	0.679002	GATGGAGCTGAGCAAAGCCA	60.679	55.000	7.39	8.99	44.68	4.75
4267	5946	1.066303	CGAGTCTGTACTGGATGGAGC	59.934	57.143	0.00	0.00	35.56	4.70
4282	5961	1.565305	CTTATGCACCTGCTCGAGTC	58.435	55.000	15.13	7.10	42.66	3.36
4305	5990	4.755629	TGGTCGAGAGGAGACTATTATTCG	59.244	45.833	0.00	0.00	44.43	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.